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- PDB-4ltn: Crystal structures of NADH:FMN oxidoreductase (EMOB) - FMN, NADH ... -

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Basic information

Entry
Database: PDB / ID: 4ltn
TitleCrystal structures of NADH:FMN oxidoreductase (EMOB) - FMN, NADH complex
ComponentsNADH-dependent FMN reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


alkanesulfonate catabolic process / FMN reductase (NAD(P)H) activity / nucleotide binding
Similarity search - Function
NADPH-dependent FMN reductase, SsuE / : / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH-dependent FMN reductase
Similarity search - Component
Biological speciesEDTA-degrading bacterium BNC1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsNissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S. / Belchik, S.M. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis.
Authors: Nissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S.Y. / Belchik, S.M. / Xun, L. / Kang, C.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionAug 7, 2013ID: 2VZJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4305
Polymers21,1161
Non-polymers1,3144
Water2,252125
1
A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules

A: NADH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,71820
Polymers84,4634
Non-polymers5,25616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area17580 Å2
ΔGint-196 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.180, 101.180, 129.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein NADH-dependent FMN reductase / EmoB


Mass: 21115.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EDTA-degrading bacterium BNC1 (bacteria)
Gene: emoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F9T2, FMN reductase (NADH)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, ...Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.996→20 Å / Num. all: 49033 / Num. obs: 23514 / Observed criterion σ(F): 2
Reflection shellHighest resolution: 1.996 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LTD

4ltd


Resolution: 1.996→19.945 Å / SU ML: 0.14 / σ(F): 4.27 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 2000 8.51 %RANDOM
Rwork0.1772 ---
obs0.1784 23511 86.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→19.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 85 125 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081521
X-RAY DIFFRACTIONf_angle_d1.0682082
X-RAY DIFFRACTIONf_dihedral_angle_d11.849538
X-RAY DIFFRACTIONf_chiral_restr0.069242
X-RAY DIFFRACTIONf_plane_restr0.004255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.996-2.04590.18051010.16621086X-RAY DIFFRACTION63
2.0459-2.10120.19911150.17031232X-RAY DIFFRACTION70
2.1012-2.16290.20081180.16531266X-RAY DIFFRACTION73
2.1629-2.23270.19941260.16941362X-RAY DIFFRACTION78
2.2327-2.31230.18851360.16651474X-RAY DIFFRACTION84
2.3123-2.40480.20561400.17771500X-RAY DIFFRACTION85
2.4048-2.5140.24411420.18561520X-RAY DIFFRACTION87
2.514-2.64630.2051470.19241586X-RAY DIFFRACTION90
2.6463-2.81160.1941530.19341648X-RAY DIFFRACTION93
2.8116-3.02810.19271550.18721672X-RAY DIFFRACTION94
3.0281-3.33150.19961610.18331713X-RAY DIFFRACTION97
3.3315-3.81070.15881640.15941765X-RAY DIFFRACTION97
3.8107-4.790.17631650.15211792X-RAY DIFFRACTION98
4.79-19.94570.20171770.20481895X-RAY DIFFRACTION97

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